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Yixuan Li

Doctorat - McGill
Superviseur⋅e principal⋅e
Archer Yang
Co-supervisor
Yue Li
Sujets de recherche
Apprentissage automatique médical
Apprentissage profond
Causalité
Traitement du langage naturel

Publications

MixEHR-SurG: a joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records
Yixuan Li
Ariane Marelli
Archer Yang
Yue Li
Survival models can help medical practitioners to evaluate the prognostic importance of clinical variables to patient outcomes such as morta… (voir plus)lity or hospital readmission and subsequently design personalized treatment regimes. Electronic Health Records (EHRs) hold the promise for large-scale survival analysis based on systematically recorded clinical features for each patient. However, existing survival models either do not scale to high dimensional and multi-modal EHR data or are difficult to interpret. In this study, we present a supervised topic model called MixEHR-SurG to simultaneously integrate heterogeneous EHR data and model survival hazard. Our contributions are three-folds: (1) integrating EHR topic inference with Cox proportional hazards likelihood; (2) integrating patient-specific topic hyperparameters using the PheCode concepts such that each topic can be identified with exactly one PheCode-associated phenotype; (3) multi-modal survival topic inference. This leads to a highly interpretable survival topic model that can infer PheCode-specific phenotype topics associated with patient mortality. We evaluated MixEHR-SurG using a simulated dataset and two real-world EHR datasets: the Quebec Congenital Heart Disease (CHD) data consisting of 8211 subjects with 75,187 outpatient claim records of 1767 unique ICD codes; the MIMIC-III consisting of 1458 subjects with multi-modal EHR records. Compared to the baselines, MixEHR-SurG achieved a superior dynamic AUROC for mortality prediction, with a mean AUROC score of 0.89 in the simulation dataset and a mean AUROC of 0.645 on the CHD dataset. Qualitatively, MixEHR-SurG associates severe cardiac conditions with high mortality risk among the CHD patients after the first heart failure hospitalization and critical brain injuries with increased mortality among the MIMIC-III patients after their ICU discharge. Together, the integration of the Cox proportional hazards model and EHR topic inference in MixEHR-SurG not only leads to competitive mortality prediction but also meaningful phenotype topics for in-depth survival analysis. The software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-SurG.
2024-05-01
Journal of Biomedical Informatics (publié)
doi.org
arxiv.org
MixEHR-SurG: a joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records
Yixuan Li
Ariane Marelli
Archer Yang
Yue Li
Survival models can help medical practitioners to evaluate the prognostic importance of clinical variables to patient outcomes such as morta… (voir plus)lity or hospital readmission and subsequently design personalized treatment regimes. Electronic Health Records (EHRs) hold the promise for large-scale survival analysis based on systematically recorded clinical features for each patient. However, existing survival models either do not scale to high dimensional and multi-modal EHR data or are difficult to interpret. In this study, we present a supervised topic model called MixEHR-SurG to simultaneously integrate heterogeneous EHR data and model survival hazard. Our contributions are three-folds: (1) integrating EHR topic inference with Cox proportional hazards likelihood; (2) integrating patient-specific topic hyperparameters using the PheCode concepts such that each topic can be identified with exactly one PheCode-associated phenotype; (3) multi-modal survival topic inference. This leads to a highly interpretable survival topic model that can infer PheCode-specific phenotype topics associated with patient mortality. We evaluated MixEHR-SurG using a simulated dataset and two real-world EHR datasets: the Quebec Congenital Heart Disease (CHD) data consisting of 8211 subjects with 75,187 outpatient claim records of 1767 unique ICD codes; the MIMIC-III consisting of 1458 subjects with multi-modal EHR records. Compared to the baselines, MixEHR-SurG achieved a superior dynamic AUROC for mortality prediction, with a mean AUROC score of 0.89 in the simulation dataset and a mean AUROC of 0.645 on the CHD dataset. Qualitatively, MixEHR-SurG associates severe cardiac conditions with high mortality risk among the CHD patients after the first heart failure hospitalization and critical brain injuries with increased mortality among the MIMIC-III patients after their ICU discharge. Together, the integration of the Cox proportional hazards model and EHR topic inference in MixEHR-SurG not only leads to competitive mortality prediction but also meaningful phenotype topics for in-depth survival analysis. The software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-SurG.
2023-12-20
ArXiv (prépublication)
doi.org
arxiv.org
Novice Type Error Diagnosis with Natural Language Models
Chuqin Geng
Haolin Ye
Yixuan Li
Tianyu Han
Brigitte Pientka
Xujie Si
Strong static type systems help programmers eliminate many errors without much burden of supplying type annotations. However, this flexibili… (voir plus)ty makes it highly non-trivial to diagnose ill-typed programs, especially for novice programmers. Compared to classic constraint solving and optimization-based approaches, the data-driven approach has shown great promise in identifying the root causes of type errors with higher accuracy. Instead of relying on hand-engineered features, this work explores natural language models for type error localization, which can be trained in an end-to-end fashion without requiring any features. We demonstrate that, for novice type error diagnosis, the language model-based approach significantly outperforms the previous state-of-the-art data-driven approach. Specifically, our model could predict type errors correctly 62% of the time, outperforming the state-of-the-art Nate's data-driven model by 11%, in a more rigorous accuracy metric. Furthermore, we also apply structural probes to explain the performance difference between different language models.
2022-10-07
ArXiv (prépublication)
doi.org
arxiv.org